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- PDB-7ots: Crystal structure of human Monoacylglycerol Lipase ABHD6 in compl... -

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Basic information

Entry
Database: PDB / ID: 7ots
TitleCrystal structure of human Monoacylglycerol Lipase ABHD6 in complex with oleic acid and octyl glucoside
ComponentsMonoacylglycerol lipase ABHD6
KeywordsHYDROLASE / alpha/beta-Hydrolase domain containing 6 / 2-arachidonoylglycerol hydrolase / monoacylglycerol lipase ABHD6 / endocannabinoid system / 2-AG signalling / nervous system
Function / homology
Function and homology information


lysobisphosphatidic acid metabolic process / : / Arachidonate production from DAG / acylglycerol catabolic process / acylglycerol lipase / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / phospholipase activity / monoacylglycerol lipase activity / phospholipid catabolic process ...lysobisphosphatidic acid metabolic process / : / Arachidonate production from DAG / acylglycerol catabolic process / acylglycerol lipase / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / phospholipase activity / monoacylglycerol lipase activity / phospholipid catabolic process / negative regulation of cold-induced thermogenesis / long-term synaptic depression / AMPA glutamate receptor complex / GABA-ergic synapse / positive regulation of lipid biosynthetic process / negative regulation of cell migration / mitochondrial membrane / late endosome membrane / membrane => GO:0016020 / lysosomal membrane / glutamatergic synapse / mitochondrion / plasma membrane
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
OLEIC ACID / Monoacylglycerol lipase ABHD6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsNawrotek, A. / Talagas, A. / Vuillard, L. / Miallau, L.
CitationJournal: To Be Published
Title: Crystal structure of human Monoacylglycerol Lipase ABHD6 in complex with oleic acid and octyl glucoside
Authors: Nawrotek, A. / Talagas, A. / Vuillard, L. / Miallau, L.
History
DepositionJun 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monoacylglycerol lipase ABHD6
B: Monoacylglycerol lipase ABHD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,91811
Polymers67,4962
Non-polymers1,4229
Water5,278293
1
A: Monoacylglycerol lipase ABHD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5155
Polymers33,7481
Non-polymers7674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monoacylglycerol lipase ABHD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4036
Polymers33,7481
Non-polymers6555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.815, 71.494, 77.83
Angle α, β, γ (deg.)90, 111.11, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Monoacylglycerol lipase ABHD6 / 2-arachidonoylglycerol hydrolase / Abhydrolase domain-containing protein 6


Mass: 33748.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABHD6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BV23, acylglycerol lipase
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 301 molecules

#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate, 35 % PEG 3350, 0.1 M MES pH 6.5, 0.5% beta-OG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.766→72.6 Å / Num. obs: 41378 / % possible obs: 91.7 % / Redundancy: 4.8 % / CC1/2: 0.985 / Net I/σ(I): 5.3
Reflection shellResolution: 1.776→1.93 Å / Rmerge(I) obs: 0.923 / Num. unique obs: 2071 / CC1/2: 0.457 / Rpim(I) all: 0.54 / Rrim(I) all: 1 / % possible all: 47.7

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OPM

4opm


Resolution: 1.792→72.61 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.886 / SU R Cruickshank DPI: 0.237 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 1921 -RANDOM
Rwork0.2222 ---
obs0.2243 39001 66.6 %-
Displacement parametersBiso mean: 23.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.8388 Å20 Å2-0.5395 Å2
2--0.906 Å20 Å2
3---0.9328 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.792→72.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 0 93 293 4973
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094928HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.986706HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1785SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes817HARMONIC5
X-RAY DIFFRACTIONt_it4871HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion608SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4238SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion16.68
LS refinement shellResolution: 1.792→1.9 Å
RfactorNum. reflection% reflection
Rfree0.4203 44 -
Rwork0.2686 --
obs--8.47 %

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